ENST00000512652.1:n.846-501C>T

Variant names:

• chr4-160585745-C-T
• rs17291045
• ENST00000512652.1:n.846-501C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000512652.1(LINC02477):​n.846-501C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0939 in 152,144 control chromosomes in the GnomAD database, including 907 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.094 (907 hom., cov: 32)
• Consequence: LINC02477 ENST00000512652.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 14 publications found

Genes affected

LINC02477 (HGNC:53425): (long intergenic non-protein coding RNA 2477)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512652.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02477	ENST00000512652.1	TSL:5	n.846-501C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0940 AC: 14286 AN: 152028 Hom.: 907 Cov.: 32

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0536

Gnomad SAS AF: 0.0845

Gnomad FIN AF: 0.0882

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.109

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0939 AC: 14293 AN: 152144 Hom.: 907 Cov.: 32 AF XY: 0.0919 AC XY: 6835 AN XY: 74386

African (AFR) AF: 0.0235 AC: 976 AN: 41538

American (AMR) AF: 0.109 AC: 1664 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3470

East Asian (EAS) AF: 0.0541 AC: 280 AN: 5174

South Asian (SAS) AF: 0.0850 AC: 410 AN: 4822

European-Finnish (FIN) AF: 0.0882 AC: 935 AN: 10598

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.129 AC: 8744 AN: 67984

Other (OTH) AF: 0.110 AC: 232 AN: 2106

Alfa AF: 0.119 Hom.: 3963

Bravo AF: 0.0945

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.79
DANN	Benign	0.44
PhyloP100		-0.062

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17291045; hg19: chr4-161506897;